title: TAX1BP1-KO-2

city: Zhanjiang

first: Ji-Xin

last: Tang

state: Guangdong

address: No.57, Renmin Avenue

institute: Affiliated Hospital of Guangdong Medical University

description: KODMSO2 TPM' and ‘KODMSO2 Read Count’

data_processing:
Transcriptome sequencing procedures include RNA extraction, RNA sample quality detection, library construction, library purification, li-brary detection, library quantification, generation of sequencing clusters, and comput-er sequencing. In order to ensure the accuracy and reliability of source data, we carried out strict quality control for each step of the experimental process.
Different libraries were mixed according to the requirements of effective concen-tration and target data volume and then sequencing by Illumina.
Bcl2fastq (v2.17.1.14) was used for image Base Calling for preliminary quality analysis to obtain the original sequencing Data (Pass Filter Data), and the results were stored in FASTQ file format. It contains sequencing sequence information and its corresponding sequencing quality information. The sequencing data quality was evaluated by FastQC (v0.10.1) software.
Raw data was preprocessed using Cutadapt (version 1.9.1) software and low quality data was filtered to remove contamination and joint sequences. The filtered sequenc-ing Clean Data was compared with the reference genome for analysis.
Hisat2(v2.0.1) software was used to compare short reads with the default parameters. Gene expres-sion was calculated using Cuffdiff software (v2.2.1), which calculated gene expression using TPM[38]. Genetic difference anal-ysis was performed using cuffdiff(v2.2.1), which was based on a negative binomial distribution model. The detection results were screened according to the differential significance criteria (differential gene expression changes of more than 2 times and qvalue(fdr, padj<=0.05), and the down-regulation of significant differential gene ex-pression was counted.
Assembly: Homo_sapiens.GRCh37
Supplementary files format and content: matrix-CON-TAX1BP1 KO.xls contains the count value and TPM value of each sample, and the corresponding geme ID.
Supplementary files format and content: fastq.gz are the original sequencing data of the corresponding sample.

extract_protocol:
Total cellular RNA was extracted from cultured cells using RNAiso Plus (Takara, 9108, Japan) according to the manufacturer’s protocol.
The RNA concentra-tion and purity were quantified using NanoDrop 2000 ultrafine spectrophotometer (Thermo Scientific, Massachusetts, America). And then the genome DNA was elimi-nated with the RNase-free DNase H. The RNA was then reverse-transcribed with 5× FastKing-RT SuperMix kit (TIANGEN, KR118–01, Beijing, China) according to the manufacturer’s protocols. The reverse-transcribed cDNA was used as template for qPCR using Genious 2X SYBR Green Fast qPCR Mix (ABclonal, RK21204) according to the manufacturer’s protocol. LightCycler 480 II real-time fluorescence quantitative PCR instrument was used for PCR reaction. The primer sequences used for amplifying the target fragments and GAPDH as internal control were listed in Table1. Gene’s rela-tive expression levels were calculated by the 2-ΔΔCt (threshold cycle) method.

value: gene knock out cell

value: normal


title: T-cells of healthy donors, 72h stimulation + H2O2 treatment, donor 4 [H2O2.K384]

status: Public on May 01 2024

type: SRA

city: Würzburg 97074

first: Chunguang

last: Liang

state: Bayern

address: Bioinformatik, Biozentrum, Uni Würzburg, Am Hubland

department: Bioinformatics

country: Germany

institute: Biozentrum

description: read length: 2 x 150 bp

library_source: transcriptomic

data_processing:
Adapters were clipped by trim_galore
Sequence reads were mapped by STAR aligner
Counting with featureCounts
Analysed using edgeR, normallized with TMM method
Supplementary files format and content: GRCh38
Supplementary files format and content: Tab-delimited normalized cpm

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood

growth_protocol: purified human T-cells were cultured in RPMI 1640 (Thermo Fischer, Waltham, MA, USA) supplemented with GlutaMAX, P/S and 10% FCS

extract_protocol:
RNA was extracted using  the innuPREP DNA/RNA Mini Kit (Analytik Jena AG, Jena, Germany); on column DNAse digestion was used to remove genomic DNA contamination (RNAse-Free DNase Set, Qiagen, Venlo, Netherlands). RNA was diluted in RNase free H2O to a maximum concentration of 200 ng/μl.
RNAseq was performed by Eurofins/GATC Biotech (INVIEW NGS transcriptome explore). Library preparation: Strand specific cDNA library; Purification of poly-A containing mRNA molecules, mRNA fragmentation, random primed cDNA synthesis (strand specific), adapter ligation and adapter specific PCR amplification.

treatment_protocol: T-cells were incubated for 72 h with activating anti-CD2/CD3/CD28 microbeads in a 1:2 bead-to-cell ratio (Miltenyi Biotec). 10 µM H2O2 (Sigma-Aldrich, St. Louis, MO, USA) was added twice per day.

tag: disease state

value: healthy donor

tag: tissue

value: peripheral blood

tag: cell type

value: primary T-cells

tag: treatment


title: TAX1BP1-KO-1

country: China

description: KODMSO1 TPM' and ‘KODMSO1 Read Count’

tag: cell line

tag: genotype


title: RP149_347_IRP2_+/+_ZT5_Rep3_RPF

city: Lausanne

first: Hima

middle: Priyanka

last: Nadimpalli

address: Génopode Building, Room 500

country: Switzerland

institute: UNIL - CIG

library_source: other

data_processing:
Read adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were trimmed using cutadapt (v 3.5) with the following options: --match-read-wildcards --overlap 8 --discard-untrimmed --minimum-length 30 and reads were quality filtered using fastx_toolkit (-Q33 -q 30 -p 90).
Trimmed read sequences were filtered by their size using an in-house Python script with following inclusive ranges: [26,35] for footprints, [21,60] for total RNA.
Reads were then mapped to rRNA and tRNA databases to remove contaminants using bowtie2 (-p 2 -L 15 -k 20 --no-unal -q).
Only reads that did not map to the above databases were mapped to mouse genome v38.100 using STAR (version 2.70f).
Assembly: mouse genome v38.100
Library strategy: Ribo-seq

molecule: other

organism: Mus musculus

extract_protocol:
For ribosome profiling, frozen liver tissues from individual mice were homogenized with 5-6 strokes using a Teflon homogenizer in 3 volumes of polysome buffer (150 mM NaCl, 20 mM Tris-HCl pH7.4, 5 mM MgCl2, 5 mM DTT, complete EDTA-free protease inhibitors (Roche) and 40 U/ml RNasin plus (Promega)) supplemented with 1% Triton X-100 and 0.5% Na deoxycholate. Liver lysates were incubated on ice for 10 min and cleared by centrifugation at 10000g, 4°C for 10 min. For each sample, 15 OD260 of liver lysate was digested with RNase I (Ambion) for 45 min at RT under gentle agitation and passed over size exclusion columns for ribosome purification prior to RNA extraction and library preparation.
Libraries from ribosome-protected fragments (RPF) and total RNA were prepared as described in Janich et al., 2015 with few modifications. 1 µg of RPF and total RNA samples were depleted of ribosomal RNA using RiboCop rRNA depletion kit V1.3 (Lexogen). Subsequent steps were performed according to Illumina TruSeq Ribo-Profile protocol.

value: liver

value: WT

tag: time


title: TAX1BP1-KO-3

description: KODMSO3 TPM' and ‘KODMSO3 Read Count’


title: Sample 1_SF7761, RNA-seq, DMSO

city: Gdansk

first: Jakub

last: Mieczkowski

address: Debinki 12

country: Poland

institute: Medical University of Gdansk

data_processing:
RNAseq: The sequenced paired-end reads were mapped to hg38 genome using tophat2 aligner v2.1.1 with the default parameters. The expression estimates for each gene were obtained using Bioconductor package DESeq2. TPM (Transcripts per Kilobase Million) values were calculated
ChIPseq: The paired-end fragments were generated. Reads were mapped to the to hg38 genome using Bowtie aligner version 0.12.9. Only uniquely mapped reads were retained. The reads with insert sizes <50 bp or >500 bp were removed from further analysis. Genomic positions with the numbers of mapped tags above the significance threshold of Z-score of 7 were identified as anomalous, and the tags mapped to such positions were discarded. H2A.Z, H3.3 and H3.3K27M occupancies were estimated as tag frequencies
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each RNA-seq sample
Supplementary files format and content: ChIPseq: wig files with coverage

molecule: polyA RNA

source_name: brain

extract_protocol:
RNA-seq: RNA was isolated using RNeasy Plus Kit (Qiagen) according to manufacturer’s instructions and the quality was assessed with the Agilent 2100 Bioanalyzer with an RNA 6000 Pico Kit (Agilent Technologies).
RNA-seq: PolyA-enriched RNA libraries were prepared with the KAPA Stranded mRNA Sample Preparation Kit (Kapa Biosystems).
ChIP-seq: ChIP-seq (including crosslinikng, cell lysis, chromatin digestion with Mnase, and chromatin immunoprecipitatation with H3.3 and H3.3K27M antibodies) was performed based on protocol by Cook et al.., 2017 (doi: 10.1002/cpmb.45). Eluted and input DNA was purified with phenol-chloroform extraction followed by additional purification with ZymoResearch DNA Clean & Concentrator-5 columns. Digested DNA profiles were confirmed using the 2100 Bioanalyzer with the Agilent DNA High Sensitivity chip (Agilent Technologies).
ChIP-seq: The Input and ChIP libraries were prepared using the Qiaseq Ultra Low Input Library Kit (Qiagen), according to manufacturer’s instructions.

value: brain

value: H3.3K27M mutant

value: DMSO


title: Sample 2_SF7761, RNA-seq, SB939


title: T-cells of healthy donors, 72h stimulation + H2O2 treatment, donor 1 [H2O2.K374]

description: read length: 2 x 150 bp


title: CON-3

description: CONDMSO3 TPM' and ‘CONDMSO3 Read Count’

value: normal cell


title: T-cells of healthy donors, control, 72h stimulation, donor 1 [Ctrl.K374]

description: read length: 2 x 150 bp

value: untreated


title: TR109_340_IRP1_ko/ko_ZT12_Rep2_totalRNA

data_processing:
Read adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were trimmed using cutadapt (v 3.5) with the following options: --match-read-wildcards --overlap 8 --discard-untrimmed --minimum-length 30 and reads were quality filtered using fastx_toolkit (-Q33 -q 30 -p 90).
Trimmed read sequences were filtered by their size using an in-house Python script with following inclusive ranges: [26,35] for footprints, [21,60] for total RNA.
Reads were then mapped to rRNA and tRNA databases to remove contaminants using bowtie2 (-p 2 -L 15 -k 20 --no-unal -q).
Only reads that did not map to the above databases were mapped to mouse genome v38.100 using STAR (version 2.70f).
Assembly: mouse genome v38.100

value: IRP1 Knockout


title: CON-2

description: CONDMSO2 TPM' and ‘CONDMSO2 Read Count’


title: Umbilical mesenchymal stem cell derived exosome_rep3

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

description: small extracellular vesicles

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: excel,expression profiles

source_name: Umbilical mesenchymal stem cell

growth_protocol: 1%FBS low-glucose DMEM were used as culture medium for mesenchymal stem cell and osteoblast cell culture, while embryonic stem cells were cultured using PSGro serum-free medium. 1% FBS were used to generate differentiation of embryonic stem cells. When cells reach 70% confluent, the cells were ready to perform exosome collection. For exosome collection, the medium were collected at a 3-days interval for exosome collection.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: No specific treatment were done during the sample collection.

value: Umbilical mesenchymal stem cell


title: RP148_340_IRP2_ko/ko_ZT5_Rep3_RPF

value: IRP2 knockout


title: RP149_340_IRP2_+/+_ZT5_Rep3_RPF


title: Si-NC-LINC00882

city: Jiaxing

first: Huadong

last: Ni

address: zhonghuan nan road 1882

institute: Department of Anesthesiology and Pain Research Center, The Affiliated Hospital of Jiaxing University

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8)
Sequence quality was examined using the FastQC software(v0.11.7)
The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt(v1.17)) were aligned to reference genome(GRCh37) using Hisat2 software(v2.1.0)
The transcript abundance for each sample was estimated with StringTie(v1.3.3), and the FPKM value for gene and transcript level was calculated with R package Ballgown(v2.10.0)
Assembly: GRCh37
Supplementary files format and content: the FPKM value of detected mRNA for each sample

source_name: breast

growth_protocol: Cells were cultured L15 culture medium with 10% FBS

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
LINC00882 was knocked down by respectivly transfection with  LINC00882 siRNA  in 231 cells
EZ-Magna RIP Kit (Millipore, USA) was used in RIP assay following the manufacturer’s protocols. MDA-MB-231 cells  were lysed with RIP lysis buffer, followed by incubated with RIP buffer containing magnetic beads conjugated with human anti-PABPC1 antibody, and IgG (Millipore).

value: breast

value: 231 cell

value: control


title: TR108_340_IRP1_+/+_ZT12_Rep1_totalRNA


title: CON-1

description: CONDMSO1 TPM' and ‘CONDMSO1 Read Count’

value: normal


title: G_WT_2

city: Oslo

first: Mingyi

last: Yang

address: Sognsvannsveien 20

department: Department of Microbiology, Rikshospitalet

country: Norway

institute: Oslo University Hospital

library_source: genomic

data_processing:
GWBS (bisulfite seq) -- The reads were aligned to reference mice genome GRCm38 , following to extract genome-wide 5mC in context of CG, CHG and CHH using Bismark tool. methylKit was used to quantify levels of methylated bases and to identify differently methylated cytosines, regions and promoters (DMC, DMR and DMP). The methylation profile and DMRs in gene feature regionsTSS, TES and gene body were analysed by a Python package HMST-Seq-Analyzer pipeline.
RNA-seq --  The clean reads were aligned to reference mouse genome mm10/GRCm38 by HISAT. The transcripts from all samples were futher assembled and merged using stingTie. The DESeq2 tool was used to normalize counts and identify the differentially expressed genes.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: 5mC percentage in CG context
Supplementary_files_format_and_content: transcript count table in FPKM
Supplementary_files_format_and_content: normalized count by DESeq2

molecule: genomic DNA

source_name: hippocampus

extract_protocol: GWBS: total DNA was extracted from hippocampus of male mice using a AllPrep DNA/RNA/Protein mini-Kit, following by bisulfite treatment and library preparision. RNA-seq: RNA extracted by AllPrep DNA/RNA/Protein mini-Kit.

tag: strain background

value: hippocampus

tag: age

value: post natal 6 months

tag: genotype/variation

value: wild type


title: MDA-MB-231 cells, PVT1-3

city: Nanjing

first: Xingxing

last: Li

state: Jiangsu

address: 123 Tianfei Road

institute: Women’s Hospital of Nanjing Medical University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)
Removing reads containing sequencing adapter;
Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%;
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12) .

growth_protocol: Cells were grown in Dulbecco’s Modified Eagle’s Medium (Gibco, USA) supplemented with 10% FBS and 1% penicillin-streptomycin mixture and incubated at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from NC and PVT1 overexpressed MDA-MB-231 cells by using TRIzol reagent (Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transduced with PVT1 lentiviral construct (pLVX-PVT1-EF1α-IRES-EGFP-PGK-puro) or with negative controls (empty vector).

tag: overexpression


title: RP147_340_IRP2_+/+_ZT5_Rep2_RPF

value: liver


title: RP147_347_IRP2_+/+_ZT5_Rep2_RPF

value: WT


title: Umbilical mesenchymal stem cell derived exosome_rep2

description: small extracellular vesicles


title: 231-PABPC1

description: EZ-Magna RIP Kit (Millipore, USA) was used in RIP assay following the manufacturer’s protocols. MDA-MB-231 cells  were lysed with RIP lysis buffer, followed by incubated with RIP buffer containing magnetic beads conjugated with human anti-PABPC1 antibody, and IgG (Millipore).

value: anti-PABPC1 antibody


title: Umbilical mesenchymal stem cell derived exosome_rep1

description: small extracellular vesicles


title: MDA-MB-231 cells, PVT1-2


title: MDA-MB-231 cells, PVT1-1


title: RP146_340_IRP2_ko/ko_ZT5_Rep2_RPF


title: IL-1b treated Human Osteoblast derived exosome_rep1

description: small extracellular vesicles

source_name: Osteoblast

value: Osteoblast


title: RP146_347_IRP2_ko/ko_ZT5_Rep2_RPF


title: KOPN cells, sgRNA SETD2 clone BA, single cell clone A6 after treatment

city: New York

first: Sonali

last: Narang

state: NY

address: 435 east 30th street

country: USA

institute: NYU Langone

data_processing:
Trim adapters and low quality bases using Trimmomatic
Align to the reference genomehg19 using BWA
Call variants using Strelka variant caller
Assembly: hg19
Supplementary files format and content: txt files containing variant info from Strelka variant caller

growth_protocol: The B-lineage leukemia cell lines KOPN-8 and 697 (DSMZ, Braunschweig, Germany) were grown in RPMI1640 medium supplemented with 10% FBS, 1% penicillin/streptomycin under 5% CO2 at 37°C. No cell lines were used beyond passage 20.

extract_protocol:
Genomic DNA was harvested using QIAGEN DNeasy Blood and Tissue Kit
WES libraries were generated using Nextera Flex for Enrichment Prep.
WES-seq

treatment_protocol: SETD2 KO and  WT KOPN-8 cells were single cell cloned and 3 sub clones from each group were subsequently treated with 6-TG for 9 days. Following treatment, DNA was extracted from the treated cells as well as the pre-treated clones

value: B-ALL cell line

value: SETD2 heterozygous KO

value: 9 days of 0.15mM 6TG

value: Day 9


title: Si-LINC00882

description: LINC00882 was knocked down by transfection with LINC00882 Smart Silencer

value: LINC00882 knocked down


title: KOPN cells, sgRNA SETD2 clone BA, single cell clone A3 after treatment


title: IL-1b treated Human Osteoblast derived exosome_rep2

description: small extracellular vesicles


title: IL-1b treated Human Osteoblast derived exosome_rep3

description: small extracellular vesicles


title: Human Osteoblast derived exosome_rep3

description: small extracellular vesicles


title: MDA-MB-231 cells, NC2

value: empty vector


title: RP145_347_IRP2_+/+_ZT5_Rep1_RPF


title: KOPN cells, sgRNA SETD2 clone BA, single cell clone A6

value: pre treatment

value: Day 0


title: Human Osteoblast derived exosome_rep2

description: small extracellular vesicles


title: KOPN cells, sgRNA SETD2 clone BA, single cell clone A1 after treatment


title: MDA-MB-231 cells, NC3


title: RP144_340_IRP2_ko/ko_ZT5_Rep1_RPF

value: IRP2 knockout


title: MDA-MB-231 cells, NC1


title: KOPN cells, sgRNA SETD2 clone BA, single cell clone A3


title: 231-Input

value: breast

value: 231 cell

value: input


title: RP135_347_IRP2_+/+_ZT12_Rep3_RPF


title: Human Osteoblast derived exosome_rep1

description: small extracellular vesicles


title: mESC 14, nuclei, m6dA methylated, rep8

city: San Francisco

first: Arjun

middle: S

last: Nanda

state: California

address: 1700 Owens St

department: Gladstone Institute for Data Science & Biotechnology

institute: Gladstone Institutes / UCSF

data_processing:
Demultiplexing subreads BAM files with lima (v2.6.0)
Generating circular consensus sequences (CCS) using ccs (v6.4.0) with kinetic information
Extracting kinetic information from CCS reads using the SAMOSA-ChAAT computational pipeline
Aligning CCS reads to the mm10 reference genome using pbmm2 (v.1.9.0)
Assembly: mm10
Supplementary files format and content: *_full.pickle: Python pickle files containing IPD measurements for each base in the forward and reverse strands per CCS read
Supplementary files format and content: *_zmwinfo.pickle: Python pickle containing a  dataframe with length, # of  passes, and mean IPD per base per CCS read

source_name: mouse embryonic stem cell E14

growth_protocol: Feeder-free E14 mouse embryonic stem cells (mESC E14)  cultures were maintained on 0.2% gelatin, in KnockOut DMEM 1X (Gibco) supplemented with 10% Fetal Bovine Serum (Phoenix Scientific), 1% 100X GlutaMAX (Gibco), 1% 100X MEM Non-Essential Amino Acids (Gibco), 0.128mM 2-mercaptoethanol (BioRad), and 1X Leukemia Inhibitory Factor. Cultures were passaged at least twice before use.

extract_protocol:
Tagmented nuclei were pre-treated with 10uL RNaseA at 37°C for 15 minutes, then purified with 2.5uL Proteinase K (20mg/mL), 2.5uL 10% SDS, and 2.5uL 0.5mM EDTA at 60°C for 1-2 hours with continuous shaking at 1000 rpm. DNA was extracted with 2x SPRI bead cleanup.
Tagmented fragments were gap-repaired using Phusion DNA polymerase and Taq Ligase at 37ºC for 1hr, digested with Exonuclease III at 37ºC for 1hr, then cleaned up using Ampure PB. Library quality was assessed with Qubit 1x High Sensitivity DNA Assay and Agilent Bioanalyzer High Sensitivity DNA kit.

treatment_protocol:
Isolated mESC E14 nuclei were methylated (10uL EcoGII per 1-2e6 nuclei) with non-specific adenine methyltransferase EcoGII (New England Biolabs, HC stock 2.5e4U/mL) at 37°C for 30 minutes, supplemented with SAM to 1.16mM (NEB) after 15 minutes.
Isolated nuclei were tagmented with H-Tn5-R27S,E54K,L372P (QB3 MarcoLab) at 55°C for 1hr.

value: mouse embryonic stem cell E14

value: mouse embryonic stem cell

value: m6dA methylated


title: Differentiated Embryonic Stem cell H9 derived exosome_rep3

description: small extracellular vesicles

source_name: Embryonic stem cell strain H9

value: Embryonic stem cell strain H9


title: mESC E14, nuclei, m6dA methylated, ex situ SAMOSA-Tag

extract_protocol:
Tagmented nuclei were pre-treated with 10uL RNaseA at 37°C for 15 minutes, then purified with 2.65uL Proteinase K (20mg/mL), and 2.65uL 10% SDS at 65°C for 3 hours. DNA was extracted using an equal volume of phenol:chloroform:isoamyl Alcohol (25:24:1, v/v), followed by 100% ethanol percipitation overnight at -80ºC.
Extracted DNA was tagmented using SMRT-Tag conditions (in 1X Tagmentation Mix (10mM TAPS-NaOH pH 8.5, 5mM MgCl2, and 10% DMF) , 55ºC for 30 min) with 0.046 pmol H-Tn5-R27S,E54K,L372P (QB3 MarcoLab) , then terminated  by adding 0.2% SDS (final concentration 0.04%). Tagmented fragments were gap-repaired using Phusion DNA polymerase and Taq Ligase at 37ºC for 1hr, digested with Exonuclease III at 37ºC for 1hr, then cleaned up using Ampure PB. Library quality was assessed with Qubit 1x High Sensitivity DNA Assay and Agilent Bioanalyzer High Sensitivity DNA kit.
OTHER: Ex situ SAMOSA-Tag Library Preparation

treatment_protocol: Isolated mESC E14 nuclei were methylated (10uL EcoGII per 1-2e6 nuclei) with non-specific adenine methyltransferase EcoGII (New England Biolabs, HC stock 2.5e4U/mL) at 37°C for 30 minutes, supplemented with SAM to 1.16mM (NEB) after 15 minutes.


title: KOPN cells, sgRNA SETD2 clone BA, single cell clone A1


title: RP135_340_IRP2_+/+_ZT12_Rep3_RPF

value: liver

value: WT


title: KOPN cells, sgRNA empty vector control, single cell clone H12 after treatment

value: B-ALL cell line

value: SETD2 WT


title: Differentiated Embryonic Stem cell H9 derived exosome_rep2

description: small extracellular vesicles


title: RP145_340_IRP2_+/+_ZT5_Rep1_RPF


title: Embryonic Stem cell H9 derived exosome_rep3

description: small extracellular vesicles


title: mESC 14, nuclei, m6dA methylated, rep7


title: KOPN cells, sgRNA empty vector control, single cell clone F9 after treatment

value: 9 days of 0.15mM 6TG

value: Day 9


title: RP134_340_IRP2_ko/ko_ZT12_Rep3_RPF


title: RP132_340_IRP2_ko/ko_ZT12_Rep2_RPF


title: Differentiated Embryonic Stem cell H9 derived exosome_rep1

description: small extracellular vesicles


title: mESC 14, nuclei, m6dA methylated, rep5


title: mESC 14, nuclei, m6dA methylated, rep6


title: RP131_340_IRP2_+/+_ZT12_Rep1_RPF


title: RP133_340_IRP2_+/+_ZT12_Rep2_RPF


title: KOPN cells, sgRNA empty vector control, single cell clone H12


title: KOPN cells, sgRNA empty vector control, single cell clone B10


title: RP130_340_IRP2_ko/ko_ZT12_Rep1_RPF


title: mESC 14, nuclei, m6dA methylated, rep4


title: Embryonic Stem cell H9 derived exosome_rep2

description: small extracellular vesicles


title: Embryonic Stem cell H9 derived exosome_rep1

description: small extracellular vesicles


title: KOPN cells, sgRNA empty vector control, single cell clone B10 after treatment


title: KOPN cells, sgRNA empty vector control, single cell clone F9


title: RP125_347_IRP1_+/+_ZT5_Rep3_RPF


title: KOPN cells, sgRNA SETD2 clone BA, ATAC, biol rep2

description: KOPN cells, sgRNA SETD2 clone BA, biol rep2

data_processing:
Aigned to reference genome (hg19) using Bowtie2
Filtering of duplicate reads by Sambamba
Peak-calling conducted with MACS2
Assembly: hg19
Supplementary files format and content: bed files consisting of peak calls for each sample with 2replicates, bigwig files consisiting of peak information for visualization

extract_protocol:
Cells were lysed via centrifugation for 1 minute at 500xg. Nuclei were tagmented using Nextera (Illumina) Tagmentation DNA buffer and enzyme.
libraries were prepped according to protocol by Buenrostro et al. Briefly, PCR was performed using barcoded primers that recongizne the adapter sequences inserted during the transpase reaction.

tag: chip antibody

value: SETD2 heterozygous KO


title: mESC 14, nuclei, m6dA methylated, rep3


title: Differentiated Embryonic Stem cell H1 derived exosome_rep2

description: small extracellular vesicles

source_name: Embryonic stem cell strain H1

value: Embryonic stem cell strain H1


title: Differentiated Embryonic Stem cell H1 derived exosome_rep3

description: small extracellular vesicles


title: mESC 14, nuclei, m6dA methylated, rep1


title: RP125_340_IRP1_+/+_ZT5_Rep3_RPF


title: Differentiated Embryonic Stem cell H1 derived exosome_rep1

description: small extracellular vesicles


title: RP124_340_IRP1_ko/ko_ZT5_Rep3_RPF

value: IRP1 Knockout


title: Embryonic Stem cell H1 derived exosome_rep3

description: small extracellular vesicles


title: KOPN cells, sgRNA empty vector control, ATAC, biol rep2

description: KOPN cells, sgRNA empty vector control, biol rep2


title: Cyano Fungi EM_2

city: Bangkok

first: Jidapa

last: Leksingto

country: Thailand

institute: Chulalongkorn

description: with fungi 2: The Synechocystis cultivation under BG-11 with 5 µM of erythromycin and 5 mg of fungi addition_replicated 2

data_processing:
cDNA libraries were quantified using a DeNovix fluorometer (DeNovix).
Pair-end 125 nucleotides read sequencing on an Illumina HiSeq sequencer was done with cluster creation.
The quality of the raw read data was examined using the FASTQC software.
Fastp software was used to delete adapters and low-quality reads.
Salmon software was used to compare high-quality reads to the reference genome sequence (Synechocystis sp. PCC 6803, accession number: ASM972v1). DESeq2 was used for the differential gene expression analysis (FDR 0.05, log2 fold change > 1.0)
Assembly: mm10, Synechocystis sp. PCC 6803, accession number: ASM972v1
Supplementary files format and content: fold-change
Supplementary files format and content: fold-change of transcript level

organism: Synechocystis sp. PCC 6803

source_name: total cell

growth_protocol: BG11 medium cultured for 7 day

extract_protocol:
TRIzol reagent (Life Technologies, Carlsbad, CA, USA) was used to extract RNA
In brief, RNA strand-specific RNA-Seq libraries were created using the QIAseq FastSelect RNA removal and QIAseq stranded total RNA library preparation kits (QIAGEN).
QIAseq stranded total RNA library preparation kits (QIAGEN

treatment_protocol: with and without erythromycin

value: total cell

value: wild type

value: Erythromycin + fungi


title: RP123_347_IRP1_+/+_ZT5_Rep2_RPF


title: Cyano Fungi EM_3

description: with fungi 3: The Synechocystis cultivation under BG-11 with 5 µM of erythromycin and 5 mg of fungi addition_replicated 3


title: Embryonic Stem cell H1 derived exosome_rep2

description: small extracellular vesicles


title: KOPN cells, sgRNA empty vector control, ATAC, biol rep1

description: KOPN cells, sgRNA empty vector control, biol rep1


title: RP123_340_IRP1_+/+_ZT5_Rep2_RPF


title: 697 cells, sgRNA SETD2 clone BM_B, ATAC, biol rep2

description: 697 cells, sgRNA SETD2 clone BM_B, biol rep2


title: Cyano EM_3

description: No fungi 3: The Synechocystis cultivation under BG-11 with 5 µM of erythromycin addition_replicated 3

value: Erythromycin


title: RP122_347_IRP1_+/+_ZT5_Rep1_RPF


title: 697 cells, sgRNA SETD2 clone BM_B, ATAC, biol rep1

description: 697 cells, sgRNA SETD2 clone BM_B, biol rep1


title: mESC 14, nuclei, m6dA methylated, rep2

value: mouse embryonic stem cell E14


title: KOPN cells, sgRNA SETD2 clone BA, ATAC, biol rep1

description: KOPN cells, sgRNA SETD2 clone BA, biol rep1


title: Cyano EM_2

description: No fungi 2: The Synechocystis cultivation under BG-11 with 5 µM of erythromycin addition_replicated 2


title: RP122_340_IRP1_+/+_ZT5_Rep1_RPF


title: 697 cells, sgRNA empty vector control, ATAC, biol rep1

description: 697 cells, sgRNA empty vector control, biol rep1


title: RP121_340_IRP1_ko/ko_ZT5_Rep2_RPF


title: RP120_347_IRP1_ko/ko_ZT5_Rep1_RPF


title: Cyano Fungi EM_1

description: with fungi 1: The Synechocystis cultivation under BG-11 with 5 µM of erythromycin and 5 mg of fungi addition_replicated 1


title: Cyano EM_2

description: Cyano EM_2: The Synechocystis cultivation under BG-11 with 5 µM of erythromycin addition_replicated 2


title: set5_NACER_ASO

city: Seoul

first: Sang Geon

last: Kim

state: Seoul

address: San56-1, Sillim-dong, Kwanak-gu

department: College of Pharmacy

country: South Korea

institute: Seoul National University

data_processing:
Built-in software (HCS 2.2.70) was used for basecalling.
Quality check of basecalling was done using FastQC v0.11.5 by calculating phred quality score.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic0.32, then mapped to hg19 whole genome using HISTAT2 v2.0.5 and Bowtie2 v2.2.6
Transcript assembly and calculation of normalized Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were done using StringTie v1.3.3b.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file include FPKM values for each Sample

extract_protocol:
Total RNA was extracted from cell homogenates using Trizol.
A library was prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA LT Sample Prep Kit.

value: NACER


title: KOPN cells, sgRNA SETD2 clone BA, biol rep2

data_processing:
adapters and low quality bases were trimmed using trimmomatic
data was aligned to reference genome (hg19) using STAR
counts were generated using DESeq2
Assembly: hg19
Supplementary files format and content: bigwig files and csv files containing raw and normalized count data

extract_protocol:
RNA was extracted using the QIAGEN RNeasy Mini Kit and quality was verified by an Agilent Bioanalyzer 2100
RNAseq libraries were generated using Automated stranded RNA-seq library prep, polyA selection


title: set6_NC

value: NC


title: set6_NACER_ASO


title: RP112_347_IRP1_+/+_ZT12_Rep3_RPF


title: KOPN cells, sgRNA SETD2 clone BA, biol rep1


title: set2_NC


title: set5_NC


title: Embryonic Stem cell H1 derived exosome_rep1

description: small extracellular vesicles


title: Cyano EM_3

description: Cyano EM_3: The Synechocystis cultivation under BG-11 with 5 µM of erythromycin addition_replicated 3


title: RP120_340_IRP1_ko/ko_ZT5_Rep1_RPF


title: KOPN cells, sgRNA SETD2 clone BA, biol rep3


title: without EM3

description: without EM3: The Synechocystis cultivation under normal BG-11 medium condition_replicated 3

value: No treatment


title: set2_NACER_ASO


title: RP112_340_IRP1_+/+_ZT12_Rep3_RPF

value: liver


title: Cyano EM_1

description: Cyano EM_1: The Synechocystis cultivation under BG-11 with 5 µM of erythromycin addition_replicated 1


title: Cyano EM_1

description: No fungi 1: The Synechocystis cultivation under BG-11 with 5 µM of erythromycin addition_replicated 1


title: without EM2

description: without EM2: The Synechocystis cultivation under normal BG-11 medium condition_replicated 2


title: RP111_347_IRP1_ko/ko_ZT12_Rep3_RPF


title: KOPN cells, sgRNA empty vector control, biol rep2


title: 697 cells, sgRNA empty vector control, ATAC, biol rep2

description: 697 cells, sgRNA empty vector control, biol rep2


title: without EM1

description: without EM1: The Synechocystis cultivation under normal BG-11 medium condition_replicated 1


title: RP111_340_IRP1_ko/ko_ZT12_Rep3_RPF


title: KOPN cells, sgRNA empty vector control, biol rep1


title: RP110_340_IRP1_+/+_ZT12_Rep2_RPF

value: WT


title: with erythromycin 3

data_processing:
cDNA libraries were quantified using a DeNovix fluorometer (DeNovix).
Pair-end 125 nucleotides read sequencing on an Illumina HiSeq sequencer was done with cluster creation.
The quality of the raw read data was examined using the FASTQC software.
Fastp software was used to delete adapters and low-quality reads.
Salmon software was used to compare high-quality reads to the reference genome sequence (Synechocystis sp. PCC 6803, accession number: ASM972v1). DESeq2 was used for the differential gene expression analysis (FDR 0.05, log2 fold change > 1.0)
Assembly: Synechocystis sp. PCC 6803, accession number: ASM972v1
Supplementary files format and content: TPM, NumReads

source_name: total cells

value: total cells

value: with erythromycin


title: 697 cells, sgRNA SETD2 clone BM_B, biol rep3

value: B-ALL cell line


title: RP110_347_IRP1_+/+_ZT12_Rep2_RPF


title: with erythromycin 1


title: KOPN cells, sgRNA empty vector control, biol rep3

value: SETD2 WT


title: no erythromycin 3

description: without EM_3

value: no erythromycin


title: 697 cells, sgRNA SETD2 clone BM_B, biol rep1

value: SETD2 heterozygous KO


title: RP109_347_IRP1_ko/ko_ZT12_Rep2_RPF

value: IRP1 Knockout


title: 697 cells, sgRNA SETD2 clone BM_B, biol rep2


title: 697 cells, sgRNA empty vector control, biol rep3


title: RP109_340_IRP1_ko/ko_ZT12_Rep2_RPF


title: no erythromycin 2

description: without EM_2


title: no erythromycin 1

description: without EM_1


title: RP108_347_IRP1_+/+_ZT12_Rep1_RPF


title: 697 cells, sgRNA empty vector control, biol rep2


title: with erythromycin 2


title: RP108_340_IRP1_+/+_ZT12_Rep1_RPF


title: 697 cells, sgRNA empty vector control, biol rep1


title: Aging SNL CCs+Spesolimab-2

city: Guangzhou

first: Dalin

last: Chen

address: 295 Changxing Road

institute: Guangdong Institute of Orthopedics

description: cA

data_processing:
The raw data obtained from sequencing was filtered using SOAPnuke (v1.5.6) to obtain clean data. Follow-up use of Dr. Tom's Multi-Omics Data Mining System (https://biosys.bgi.com) is used for data analysis, mapping and mining.
HISTA2 (v2.1.0)[2] software was used to align the clean data to the reference genome. Then, Ericscript (v0.5.5) was used for gene fusion detection and rMATS (v3.2.5) was used for alternative splicing and differential alternative splicing detection.
Align the clean data to the reference gene set using Bowtie2 (v2.3.4.3). Gene expression quantification was performed using RSEM (v1.3.1) software, and clustering heat maps of gene expression in different samples were plotted using pheatmap (v1.0.8).
Differential gene detection was performed using DESeq2 (v1.4.5) under conditions of Q value≤0.05 or FDR≤0.001.
GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of differential genes were performed using Phyper, and Qvalue≤0.05 was used as the threshold, which was defined as significant enrichment in candidate genes.
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: This project uses SOAPnuke, a filtering software independently developed by Shenzhen BGI, for filtering. The filtered "Clean Reads" are saved in FASTQ format.

source_name: Primary articular chondrocytes

extract_protocol:
Lyse the cells using Trizol, centrifuge and transfer the supernatant into an EP tube containing chloroform/isoamyl alcohol (24:1) and mix well. After centrifugation, transfer the supernatant into a new EP tube containing isopropyl alcohol and mix well, then let it stand for 2 hours at (-20°C). After washing, wash 3 times with 75% ethanol. Finally, discard the supernatant and absorb the remaining liquid. After drying, add 20-200 μL DEPC water to dissolve the precipitate.
After quality inspection of the RNA, the secondary structure is opened through denaturation, and oligo(dT) magnetic beads are used to enrich the mRNA. Then a fragmentation reagent is added to fragment the mRNA, a reaction system is prepared, and the reaction program is set to synthesize one-strand and two-strand cDNA. Repair the double-stranded cDNA end, add an A base to the 3' end, and connect the adapter to the cDNA. PCR amplification is then performed, and uncirculated linear DNA molecules are digested. The single-stranded circular DNA molecule is then replicated through rolling circles to form a DNA nanoball (DNB) containing multiple copies. The obtained DNBs are added to the mesh holes on the chip using high-density DNA nanochip technology, and sequenced through combined probe anchored polymerization technology (cPAS).

value: Primary articular chondrocytes

tag: condition

value: aging SNL CCs+Spesolimab


title: KLIP1 Clone K, rep2

type: RNA

city: San Antonio

first: Yidong

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: KLIP1 Clone K, rep2

hyb_protocol: Phalanx Hybridization Protocol: hybridization at 42 C overnight using the HybBag mixing system with 1X OneArray Hybridization Buffer (Phalanx Biotech), 0.01 mg/ml sheared salmon sperm DNA (Promega), at a concentration of 0.025 mg/ml labeled target

scan_protocol: Raw intensity signals for each microarray were captured using a Molecular Dynamics™ Axon 4100A scanner, measured using GenePixPro™ Software

data_processing: Median intensity, background subtracted, then quantile normalized.

label_protocol: Phalanx Labeling Protocol: RNA was converted to double-stranded cDNA and amplified using in vitro transcription that included amino-allyl UTP, and the amplified RNA product was subsequently conjugated with Cy5™ NHS ester (GE Healthcare Lifesciences, Piscataway, NJ)

growth_protocol: See publication

extract_protocol: See publication

treatment_protocol: See publication

value: MCF7 + KLIP1 transfection


title: KLIP1 Clone H, rep3

description: KLIP1 Clone H, rep3


title: KLIP1 Clone J, rep3

description: KLIP1 Clone J, rep3


title: Day 133 DSP-GFP-2

city: Boston

first: Karl

middle: Russell

last: Koehler

state: MA

address: 3 Blackfan Circle

department: Otolaryngology-Head and Neck Surgery

institute: Boston Children's Hospital-Harvard Medical School

library_source: transcriptomic single cell

data_processing:
CellRanger 3.0.2 was utilized to process the raw sequence data generated. The filtered gene-cell barcode matrices generated by CellRanger wereused for further analysis.
Seurat 3.0.0.9000 was used for data normalization, data scaling, graph-based clustering, cluster marker genes identification.
Assembly: GRCh38

source_name: Skin Organoids

growth_protocol: Culture experiments were performed with the WA25 hESC line (passage 21-47), purchased from WiCell Research Institute, and the Desmoplakin-mEGFP (DSP-GFP) hiPSC line (passage 35-51), acquired from the Allen Institute for Cell Science and the Coriell Institute44. Cells were cultured on 6-well plates coated with Vitronectin Recombinant Human Protein (Invitrogen) at a concentration of 0.5 µg/cm2. Pluripotent stem cells were maintained in Essential 8 Flex (Gibco) medium with 100 µg/ml Normocin (hereafter, E8; Invivogen). The medium was replenished every other day. Cells were passaged at ~80% confluency (generally every 4-5 days) in medium containing 10 µM Y27632 (hereafter, Y; ROCK inhibitor that inhibits apoptosis, Stemgent). WA25 cells were passaged in clusters with 0.5 mM EDTA, and DSP-GFP cells were passaged as single cells with StemPro Accutase Cell Dissociation Reagent (hereafter, Accutase; Gibco). Fresh E8 medium was replenished twenty-four hours following passage. Detailed information concerning cell line specifics as well as validation and testing is available at: https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/wa25.cmsx?closable=true and https://www.allencell.org/cell-catalog.html.

extract_protocol:
To dissociate WA25 and DSP-GFP into single cells, randomly selected day-48 organoids (n = 6 per sample), day-85 organoids (n = 6 per sample), and day-133 organoids (n = 1 per sample) were dissociated and pooled (day 48/85) from each group. Briefly, collected organoids were incubated with pre-warmed (37°C) TrypLE™ for total 8-30 min (depending on the organoid sizes and densities) in a 37°C incubator on a shaker at 65 rpm for a gentle swirl. During the incubation, the dissociation mixture was agitated every 3-10 min with gentle pipetting using wide-bore p1000 and p200 tips (Mettler-Toledo). By total 8-30 min of incubation, the tissue structure dissociated into a single cell suspension with no visible cell aggregation. Cold 3% BSA solution (Sigma-Aldrich) was added to the dissociated cell suspension in order to inactivate TrypLE enzymatic activity. The suspension was filtered through a 40 µm Flowmi™ cell strainer (Bel-Art™) in order to eliminate any debris. An additional three washes with cold 3% BSA solution were performed. Cells were resuspended in 3% BSA, and filtered through a 40 µm Flowmi™ cell strainer. Viability (live cell percentage) and live cell count was determined using Trypan Blue (used at 1:1 ratio) and Countess II. Final cell concentration was ~1,000 cells/µl and >90% viability.
Single cell 3’ RNA-seq experiments were conducted using the Chromium single cell system (10x Genomics, Inc) and the NexSeq500 or NovaSeq 6000 sequencer (Illumina, Inc). Approximately 17,000 cells (targeting for 10, 000 cells) per sample were added to a single cell master mix, following the Chromium Single Cell 3’ Reagent Kits v2 User Guide, CG00052 Ver B (10x Genomics, Inc). Day-6 samples were processed using the Version 3 Chromium Single Cell 3’ Reagent Kits. Along with the single-cell gel beads and partitioning oil in separate wells of a Single Cell A Chip, the single cell reaction mixture was loaded to the Chromium Controller for GEM generation and barcoding, followed by cDNA synthesis and library preparation. At each step, the quality of cDNA and library was examined by Bioanalyzer. The resulting library was sequenced in a custom program for 26b plus 98b paired-end sequencing on an Illumina NextSeq500 or 28b plus 91b paired-end on Illumina NovaSeq 6000 to a read depth of >30,000 reads per cell.

treatment_protocol: For differentiation, pluripotent hPSC colonies were detached from the culture dish using Accutase. Once dissociated, hPSCs were collected as a single cell suspension in E8 medium containing 10 µM Y (hereafter, E8-10Y). Cell concentration was determined with an automated cell counter (Countess™ II Automated Cell Counter; Countess II, Life Technologies); Trypan blue (Gibco) was used at a ratio of 1:1 (Trypan blue:cell suspension) to distinguish dead vs. live cells. The appropriate number of live cells needed for an experiment was transferred into E8 medium containing 20 µM Y (hereafter, E8-20Y). From the E8-20Y cell suspension, cells were distributed at a count of 3,500 cells in 100 µl per well into 96-well U-bottom plates (Thermo Scientific). Aggregation was aided by centrifugation at 110 rcf for 6 min. These cell aggregates were incubated in 37°C incubator under 5% CO2 for 48 hrs. Thus, we designated this timepoint as day -2. After 24 hrs incubation (at day -1), fresh 100 µl E8 medium was added to each well in order to dilute out Y and promote cell proliferation and aggregate growth. On day-0, to start differentiation, all cell aggregates were individually collected and transferred to new 96-well U-bottom plates in 100 µl of E6-based differentiation medium containing 2% Matrigel (Corning), 10 µM SB (Stemgent), 4 ng/ml basic-FGF (hereafter, FGF2; PeproTech), and 2.5 ng/ml BMP-4 (PeproTech) to initiate non-neural ectoderm formation. On day-3 of differentiation, to induce CNCC formation, 200 ng/ml LDN (BMP inhibitor, Stemgent), and 50 µg/ml of FGF2 were added in a volume of 25 µl per well, thus making the final volume 125 µl per well. On day-6 of differentiation, 75 µl of fresh E6 medium was added, bringing the final volume to 200 µl. Half of the media was changed (removal of 100 µl spent medium and addition of 100 µl fresh E6 medium) on days 8 and 10. On day-12, in order to induce self-assembly of epidermis, all aggregates were transferred into individual wells of 24-well low-attachment plates (Thermo Scientific) in 500 µl organoid maturation medium (OMM) containing 1% Matrigel. To maintain the aggregates in a floating culture for constant medium circulation, 24-well plates were placed on an orbital shaker shaking at a speed of 65 rpm in the 37°C incubator with 5% CO2. OMM is composed of Advanced DMEM/F12 (Gibco) and Neurobasal (Gibco) media at a 1:1 ratio, 1X GlutaMax™ (Gibco), 0.5X B-27 Minus Vitamin A (Gibco), and 0.5X N2 (Gibco) supplements, 0.1 mM 2-Mercaptoethanol (Gibco), and 100 µg/ml Normocin. On differentiation day-15, half of the spent medium was replenished (removal of 250 µl of spent medium and addition of 250 µl fresh medium) with OMM containing 1% Matrigel. Starting from day-18, half-medium was changed every three days (from day-18 to day-30) or every other day (from day-30 to day-150 or longer) with fresh OMM without Matrigel.

value: hiPSC-derived skin organoid

tag: hesc cell line

value: DSP-GFP

value: Day 133


title: RP107_340_IRP1_ko/ko_ZT12_Rep1_RPF

data_processing:
Read adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were trimmed using cutadapt (v 3.5) with the following options: --match-read-wildcards --overlap 8 --discard-untrimmed --minimum-length 30 and reads were quality filtered using fastx_toolkit (-Q33 -q 30 -p 90).
Trimmed read sequences were filtered by their size using an in-house Python script with following inclusive ranges: [26,35] for footprints, [21,60] for total RNA.
Reads were then mapped to rRNA and tRNA databases to remove contaminants using bowtie2 (-p 2 -L 15 -k 20 --no-unal -q).
Only reads that did not map to the above databases were mapped to mouse genome v38.100 using STAR (version 2.70f).
Assembly: mouse genome v38.100
Library strategy: Ribo-seq


title: Aging SNL CCs-2

description: bA

value: aging SNL CCs


title: Control CCs-2

description: aA

value: control CCs


title: 8h H U 4

city: Solna

first: susanne

last: neumann

address: Solnavägen 1

country: Sweden

institute: Karolinska Instituet

data_processing:
GLM = EdgeR using the GLM pipeline
Voom = EdgeR/limma using voom with sample weights o transform the data to be subsequently analyzed in limma
Assembly: Mus musculus, GRCm38
Supplementary files format and content: GO_pathway_analysis_gene_filtered_removeOutliers_GLM, .xlsx file containing the Gene ontology analysis based on the differential expression generated using the EdgeR Generalized linear models (GLM) method pipeline
Supplementary files format and content: DiffGeneExpAnalysis_Filtered_removeOutliers_GLM, .xlsx file containing the differential gene expression analysis using the Generalized linear models (GLM) method, as well as  Gene ID, lenght of gene, abundance, pvalues and FDRs
Supplementary files format and content: DiffGeneExpAnalysis_Filtered_removeOutliers_voom, .xlsx file containing the differential gene expression analysis using the Limma-Voom (VOOM) method, as well as  Gene ID, lenght of gene, abundance, pvalues and FDRs

source_name: NPC

growth_protocol: Primary neural precursor cells were isolated from adult female C57BL/6 mice, 5–12 weeks old, according to a modified protocol previously described by Johansson et al. [johansson CB, Momma S, Clarke DL, Risling M, Lendahl U and Frisen J. (1999). Identification of a neural stem cell in the adult mammalian central nervous system. Cell 96:25–34. Crossref, Medline, Google Scholar]

extract_protocol:
RNAeasy Kit according to manufacturers protocol
Illumina TruSeq Stranded mRNA, Poly-A selection, default, 1527, Input: RNA; Type: Illumina TruSeq Stranded mRNA; Option: Poly-A selection; 3 lanes minimum 14 mio reads, RNA,

treatment_protocol: NPCs were exposed to H2O2 at 100 μM for 1, or 8 h, or PBS was applied as sham treatment; washed; and collected. Total mRNA was isolated at these different time points during the experiment.

tag: strain

value: NPC


title: Day 133 DSP-GFP-1


title: Aging SNL CCs+Spesolimab-1

description: CA

value: WT


title: KLIP1 Clone K, rep1

description: KLIP1 Clone K, rep1


title: KLIP1 Clone H, rep2

description: KLIP1 Clone H, rep2


title: KLIP1 Clone J, rep2

description: KLIP1 Clone J, rep2


title: Day 133 WA25-3

value: hESC-derived skin organoid


title: 8h H U 3


title: Aging SNL CCs-1

description: BA


title: KLIP1 Clone J, rep1

description: KLIP1 Clone J, rep1


title: KLIP1 Clone K, rep3

description: KLIP1 Clone K, rep3


title: 8h H U 2


title: RP107_347_IRP1_ko/ko_ZT12_Rep1_RPF

extract_protocol:
For ribosome profiling, frozen liver tissues from individual mice were homogenized with 5-6 strokes using a Teflon homogenizer in 3 volumes of polysome buffer (150 mM NaCl, 20 mM Tris-HCl pH7.4, 5 mM MgCl2, 5 mM DTT, complete EDTA-free protease inhibitors (Roche) and 40 U/ml RNasin plus (Promega)) supplemented with 1% Triton X-100 and 0.5% Na deoxycholate. Liver lysates were incubated on ice for 10 min and cleared by centrifugation at 10000g, 4°C for 10 min. For each sample, 15 OD260 of liver lysate was digested with RNase I (Ambion) for 45 min at RT under gentle agitation and passed over size exclusion columns for ribosome purification prior to RNA extraction and library preparation.
Libraries from ribosome-protected fragments (RPF) and total RNA were prepared as described in Janich et al., 2015 with few modifications. 1 µg of RPF and total RNA samples were depleted of ribosomal RNA using RiboCop rRNA depletion kit V1.3 (Lexogen). Subsequent steps were performed according to Illumina TruSeq Ribo-Profile protocol.

value: liver


title: Day 133 DSP-GFP-3


title: KLIP1 Clone H, rep1

description: KLIP1 Clone H, rep1


title: KLIP1 Clone F, rep3

description: KLIP1 Clone F, rep3


title: Day 133 WA25-2


title: KLIP1 Clone F, rep2

description: KLIP1 Clone F, rep2


title: Day 133 WA25-1


title: LA4

city: Durham

first: Christopher

middle: L

last: Holley

state: NC

address: 2301 Erwin Rd

institute: Duke University

description:
LA_raw_counts.txt
LA_riboxi_score_mean.txt

data_processing:
Library strategy: RibOxi-seq
Paired end reads are first merged into single reads using bbmerge (v38.86) with a correction step (bbmerge-auto.sh ecco=t mix=t) before actual merging(bbmerge-auto.sh minoverlap=6 mininsert=20 mininsert0=20).
Partial 3' adapter is removed using cutadapt v2.10 (cutadapt --discard-untrimmed --minimum-length 20 -a CTGTAGGCACCATCAATGAC  -e 0.1 ), followed by moving the 5' random quadruplemer to read identifier line using move-umi.py from the riboxi-seq pipeline (move_umi.py -l 4 -i ATCACG -a ATCACGCTGTAGGCACCATCAATGAC -m 'pipeline'). Finally, cutadapt is used once again to remove reads that does not contain a fixed barcode at 3' end (cutadapt --discard-untrimmed --minimum-length 20 -a ATCACG -e 0.01 ).
Leishmania amazonensis MHOM/BR/71973/M2269 rRNA and small RNA transcript sequences were used to build STAR index (STAR version 2.7.5c). The Alignment was then done with STAR (STAR --outMultimapperOrder Random --outFilterMismatchNoverLmax 0.1 --alignEndsType EndToEnd --outSAMtype BAM SortedByCoordinate)
samtools is then used to index the resulting bam files before running umi_tools v1.01 to deduplicate aligned reads.
bedtools v2.29.2 was used with bamtobed option to generate bed files for each sample. The bedfiles were then loaded in R and all rows with "-" strands were removed. Reads 3' counts were calculated by summing up all rows that have the same "end" positions. Mean riboxi score for each position is then calculated by first calculating score per position for each sample (position/(average(position-1, position+1)+1)) followed by average each position across all samples.
Genome_build: Leishmania amazonensis MHOM/BR/71973/M2269
Supplementary_files_format_and_content: Raw 3' end counts
Supplementary_files_format_and_content: Mean riboxi scores

organism: Leishmania amazonensis

source_name: Leishmania cells

growth_protocol: Leishmania amazonensis parasites were grown in M199 media supplemented with 10% FBS at 27oC.

extract_protocol:
Total RNA was extracted from Leishmania cells using TRI-reagent as per manufactures protocol.
Libraries were created following the updated RibOxi-seq protocol (https://link.springer.com/protocol/10.1007%2F978-1-0716-1851-6_22). Specifically using the rRNA protocol with 1ug total RNA input for each sample

treatment_protocol: Total RNA was subjected to fragmentation using Benzonase and several steps of oxidation, β-elimination, and dephosphorylation, thus allowing the enrichment of Nm at 3'-end of fragmented RNAs.

tag: developmental stage

value: Promastigote

tag: molecule

value: Ribosomal RNA


title: Control CCs-1

description: AA


title: 1h H U 4


title: LA3


title: 1h H U 3


title: Day 48 DSP-GFP

value: Day 48


title: Vector Clone I, rep3

description: Vector Clone I, rep3

value: MCF7 + vector transfection


title: Day 48 WA25


title: LA2


title: 1h H U 2


title: LD3

description:
LD_raw_counts.txt
LD_riboxi_score_mean.txt

data_processing:
Library strategy: RibOxi-seq
Paired end reads are first merged into single reads using bbmerge (v38.86) with a correction step (bbmerge-auto.sh ecco=t mix=t) before actual merging(bbmerge-auto.sh minoverlap=6 mininsert=20 mininsert0=20).
Partial 3' adapter is removed using cutadapt v2.10 (cutadapt --discard-untrimmed --minimum-length 20 -a CTGTAGGCACCATCAATGAC  -e 0.1 ), followed by moving the 5' random quadruplemer to read identifier line using move-umi.py from the riboxi-seq pipeline (move_umi.py -l 4 -i ATCACG -a ATCACGCTGTAGGCACCATCAATGAC -m 'pipeline'). Finally, cutadapt is used once again to remove reads that does not contain a fixed barcode at 3' end (cutadapt --discard-untrimmed --minimum-length 20 -a ATCACG -e 0.01 ).
Leishmania donovani strain LD1S rRNA and small RNA transcript sequences were used to build STAR index (STAR version 2.7.5c). The Alignment was then done with STAR (STAR --outMultimapperOrder Random --outFilterMismatchNoverLmax 0.1 --alignEndsType EndToEnd --outSAMtype BAM SortedByCoordinate)
samtools is then used to index the resulting bam files before running umi_tools v1.01 to deduplicate aligned reads.
bedtools v2.29.2 was used with bamtobed option to generate bed files for each sample. The bedfiles were then loaded in R and all rows with "-" strands were removed. Reads 3' counts were calculated by summing up all rows that have the same "end" positions. Mean riboxi score for each position is then calculated by first calculating score per position for each sample (position/(average(position-1, position+1)+1)) followed by average each position across all samples.
Genome_build: Leishmania donovani strain LD1S
Supplementary_files_format_and_content: Raw 3' end counts
Supplementary_files_format_and_content: Mean riboxi scores

organism: Leishmania donovani

growth_protocol: Leishmania donovani parasites were grown in M199 media supplemented with 10% FBS at 27oC.

value: Leishmania donovani strain LD1S


title: OVCAR3 cells, ZIC2 OE vector biol rep 6

city: Edmonton

first: Laura

middle: Jiyoung

last: Lee

state: Alberta

address: 5-120 Katz Group Centre

department: Oncology

country: Canada

institute: University of Alberta

data_processing:
Sequence reads were trimmed for adaptor sequences using Skewer.
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR.
Gene-based read counts were obtained with FeatureCounts using aligned files generated with STAR.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include raw read counts for each sample.

growth_protocol: SKOV3 cells were cultured in DMEM/Hams’ F12 medium supplemented with 5% FBS. OVCAR3 cells were cultured in RMPI-1640 medium supplemented with 10% FBS in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Qiagen RNeasy Mini Kit with on-column DNAse treatment. 1.5 ug of total RNA was submitted for library generation and sequencing.
RNA libraries for RNA-seq were generated using NEB mRNA stranded Library preparation.

value: ovarian cancer cells

value: ZIC2 overexpression


title: 1h H U 1


title: LD2


title: OVCAR3 cells, ZIC2 OE vector biol rep 5


title: 8h H U 1


title: C U 4

value: sham exposure PBS


title: OVCAR3 cells, ZIC2 OE vector biol rep 4


title: KLIP1 Clone F, rep1

description: KLIP1 Clone F, rep1

value: MCF7 + KLIP1 transfection


title: C U 3


title: C U 2


title: OVCAR3 cells, ZIC2 OE vector biol rep 3


title: hs3

data_processing:
Library strategy: RibOxi-seq
Partial 3' adapter is removed using cutadapt v2.10 (cutadapt --discard-untrimmed --minimum-length 20 -a CTGTAGGCACCATCAATGAC  -e 0.1 ), followed by moving the 5' random quadruplemer to read identifier line using move-umi.py from the riboxi-seq pipeline (move_umi.py -l 4 -i ATCACG -a ATCACGCTGTAGGCACCATCAATGAC -m 'pipeline'). Finally, cutadapt is used once again to remove reads that does not contain a fixed barcode at 3' end (cutadapt --discard-untrimmed --minimum-length 20 -a ATCACG -e 0.01 ).
Trypanosoma brucei brucei TREU927 mRNA transcript sequences were used to build STAR index (STAR version 2.7.5c). The Alignment was then done with STAR (STAR --outMultimapperOrder Random --outFilterMismatchNoverLmax 0.1 --alignEndsType EndToEnd --outSAMtype BAM SortedByCoordinate)
samtools is then used to index the resulting bam files before running umi_tools v1.01 to deduplicate aligned reads.
bedtools v2.29.2 was used with bamtobed option to generate bed files for each sample. The bedfiles were then loaded in R and all rows with "-" strands were removed. Reads 3' counts were calculated by summing up all rows that have the same "end" positions. Mean riboxi score for each position is then calculated by first calculating score per position for each sample (position/(average(position-1, position+1)+1)) followed by average each position across all samples.
The processed file is then generated by filtering with a score_mean cutoff of 14 and mean_counts of 50
Genome_build: Trypanosoma brucei brucei TREU927
Supplementary_files_format_and_content: Raw 3'-end counts + mean counts + Nm scores in csv format

organism: Trypanosoma brucei

source_name: Trypanosoma brucei brucei TREU927

growth_protocol: Trypanosoma brucei parasites were grown in SDM-79 medium supplemented with 10% fetal calf serum at 27oC.

extract_protocol:
Total RNA was extracted from trypanosome cells using TRI-reagent and poly(A) RNA was enriched using four rounds of oligo dT selection.
Libraries were created following the updated RibOxi-seq protocol (https://link.springer.com/protocol/10.1007%2F978-1-0716-1851-6_22). Specifically using the mRNA procedures with 7ug polyA enriched RNA input for each sample

treatment_protocol: RNA was subjected to fragmentation using Benzonase and several steps of oxidation, β-elimination, and dephosphorylation, thus allowing the enrichment of Nm at 3'-end of fragmented RNAs.

value: Trypanosoma brucei brucei TREU927

value: Procyclic WT strain PC1313


title: hs2


title: OVCAR3 cells, ZIC2 OE vector biol rep 2


title: OVCAR3 cells, ZIC2 OE vector biol rep 1


title: Vector Clone H, rep3

description: Vector Clone H, rep3


title: C U 1


title: Vector Clone H, rep1

description: Vector Clone H, rep1


title: OVCAR3 cells, empty vector biol rep 6

value: EV


title: Vector Clone I, rep2

description: Vector Clone I, rep2


title: Vector Clone H, rep2

description: Vector Clone H, rep2


title: hs1


title: Vector Clone A, rep3

description: Vector Clone A, rep3


title: Vector Clone A, rep2

description: Vector Clone A, rep2


title: Vector Clone I, rep1

description: Vector Clone I, rep1


title: LD1


title: Exposed KO replicate 5

city: Madison

first: Thibaut

last: Rosay

state: Wisconsin

department: MMI

institute: UW Madison

data_processing:
STAR v2.5.3a was used to align trimmed reads to genome version ASM886v2 build-accession GCA_000008865.2 as the reference
RSEM v1.2.31 was used to estimate transcript abundance.
Assembly: NC_002695
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Escherichia coli

source_name: Bacteria

growth_protocol: Bacteria were grown 6h in DMEM low glucose in anaerobic conditions

extract_protocol:
Illumina Ribo-Zero Plus rRNA Depletion
stranded RNA library prep

treatment_protocol: treatment with or without 50uM Adenine

value: Bacteria

value: hha knocked out

value: Adenine 50uM


title: Exposed KO replicate 4


title: OVCAR3 cells, empty vector biol rep 4


title: Exposed KO replicate 3


title: Exposed KO replicate 2


title: Vector Clone A, rep1

description: Vector Clone A, rep1


title: OVCAR3 cells, empty vector biol rep 3


title: Parental Cell, rep2

description: Parental Cell, rep2

value: MCF7 parental


title: OVCAR3 cells, empty vector biol rep 2


title: Exposed KO replicate 1


title: OVCAR3 cells, empty vector biol rep 1


title: OVCAR3 cells, empty vector biol rep 5


title: Exposed control replicate 5

value: WT


title: Exposed control replicate 4


title: Parental Cell, rep1

description: Parental Cell, rep1


title: Exposed control replicate 2


title: Exposed control replicate 1


title: knocked-out Replicate 5


title: Parental Cell, rep3

description: Parental Cell, rep3


title: MM 5 LY6E+

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

description: Myeloma patient 5

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: GCOS1.1 software (Affymetrix, Santa Clara, CA) and normalized using conventional GCOS1.1 scaling.

label: Biotin

source_name: Multiple Myeloma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Samples are collected from bone marrow aspirates of multiple myeloma patients

value: CD138+ myeloma plasma cells

tag: status after 5 years

value: Live/Dead

value: 64 years

tag: Sex

value: Male


title: knocked-out Replicate 4

tag: tissue

tag: cell type


title: MM 5 Total

description: Myeloma patient 5


title: MM 5 LY6E-

description: Myeloma patient 5


title: knocked-out Replicate 3

tag: treatment


title: MM 4 LY6E-

description: Myeloma patient 4

value: 58 years


title: MM 3 LY6E-

description: Myeloma patient 3

value: 78 years


title: MM 4 LY6E+

description: Myeloma patient 4


title: knocked-out Replicate 2

tag: genotype


title: MM 2 LY6E-

description: Myeloma patient 2

value: 70 years

value: Female


title: MM 2 LY6E+

description: Myeloma patient 2


title: brain, Female, Pink1-/-, 983

first: Cynthia

middle: A

last: Kelm-Nelson

state: WI

address: 1300 University Avenue, 416 Medical Sciences Center

department: Surgery

institute: University of Wisconsin- Madiso

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptor sequences, contamination and low-quality reads were removed. Goblin (alpha and beta) were removed. Reads were mapped to the annotated rat (Rattus Norvegicus) genome in Ensembl.
Technical quality was determined using several parameters. Briefly, trimming software skewer was used to preprocess raw fastq files. Combined cycle base quality, per cycle base frequencies and average base quality, relative 3-Kmer diversity, Phred quality distribution, mean quality distribution, average read length and read occurrence distribution were used as additional quality control measures on the read data. Additionally, the biological coefficient of variation was estimated to be approximately 0.12.
Gene analysis was performed with the glm using the EdgeR Bioconductor Package, v. 3.9. The p-value cutoff was set to 0.05 for significance. A Benjamini-Hochberg correction was applied to control the False Discovery Rate (FDR).
RSEM approach for normalizing RNA seq data was used
Supplementary files format and content: tab-delimited text files include raw values for each sample.

organism: Rattus norvegicus

source_name: brain

extract_protocol:
Brains were dissected, flash frozen on dry ice, and RNA was harvested using the Bio-Rad Aurum Total RNA Fatty and Fibrous Tissue Kit (732-6830; Bio-Rad, Hercules, CA, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

value: 8 months


title: knocked-out Replicate 1


title: Exposed control replicate 3


title: brain, Female, WT, 980


title: MM 1 LY6E-

description: Myeloma patient 1

value: 60 years


title: brain, Female, Pink1-/-, 736


title: MM 2 Total

description: Myeloma patient 2


title: control replicate 5


title: control replicate 4


title: brain, Female, Pink1-/-, 602


title: control replicate 3


title: MM 1 LY6E+

description: Myeloma patient 1


title: MM 3 LY6E+

description: Myeloma patient 3


title: MM 1 Total

description: Myeloma patient 1


title: GFWT6 colon

city: Saint-Malo

first: Phuong

middle: Hang

last: PHAM

address: 7 allée Métis

department: Data science

country: France

institute: Parean Biotechnologies

description:
Gene expression at day 7 after induction of DSS colitis
GFWT06

hyb_protocol: Samples were hybridized to SurePrint G3 mouse GE 8x60K (G4858A-028005) arrays and scanned by G2565CA Scanner System (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the  Agilent DNA Microarray Scanner (G2505C) using one color scan setting for  1x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye  channel is set to Green and Green PMT is set to 100%).

data_processing: Image analyses and raw signal intensities were  quantified by Feature Extraction Software v10.7.3.1 (Agilent Technologies)  according to the GE1_107_Sep09 protocol.

source_name: Germ Free Colon

label_protocol: Labelling of total RNA (100ng) was performed with the One-Color Low Input Quick Amp Labelling kit (Agilent Technologies).

extract_protocol: Total RNA was prepared from total tissue of colon by using the column-based RNeasy® Mini Kit (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Samples with RNA integrity number (RIN) greater than 9 were selected for further analysis.

treatment_protocol: To induce colitis, mice were administered drinking water supplemented with 2% (wt./vol.) dextran sulfate sodium (DSS; MP Biomedicals, LLC, Aurora, OH, USA) for 7 d and were then allowed to recover by drinking unsupplemented water for the next 5 d

value: Colon

tag: gender

value: male

tag: stran

value: Germ-free C57BL/6J WT

value: DSS

tag: time


title: GFWT5 colon

description:
Gene expression at day 7 after induction of DSS colitis
GFWT05


title: GFWT4 colon

description:
Gene expression at day 7 after induction of DSS colitis
GFWT04


title: GFWT1 colon

description:
Gene expression at day 7 after induction of DSS colitis
GFWT01


title: GFKO4 colon

description:
Gene expression at day 7 after induction of DSS colitis
GFKO04

value: Germ-free Card9−/− C57BL/6J


title: brain, Female, WT, 504

tag: age

value: WT


title: brain, Female, WT, 111


title: control replicate 1

value: Bacteria


title: Bottom3

city: Bologna

first: Camilla

last: Luni

address: Via Terracini 28

department: DICAM

country: Italy

institute: University of Bologna

data_processing:
Illumina binary base call (BCL) files were converted into fastq file format by Illumina bcl2fastq software (v. 2.17).
Paired reads were merged using Pear (v. 0.9.11), and trimmed using cutadapt (v. 2.8).
The trimmed reads were mapped to the human GeCKOv2 library by Bowtie (v. 1.2.3).
The sgRNA count matrix was obtained from Bowtie output sam files.
Data from each sample were merged into a single table of unfiltered counts with R software (v. 4.2.2).
Assembly: Human Genome-Scale CRISPR Knock-Out (GeCKO) lentiviral pooled library (GeCKO v2, library A, cat. 1000000048, Addgene)
Supplementary files format and content: Tab delimited file containing the unfiltered counts from Bowtie alignment

growth_protocol: HFF were maintained in Dulbecco's modified Eagle Medium (DMEM, cat. 11965, ThermoScientific) supplemented with 15% fetal bovine serum (FBS, ThermoScientific) at 37°C and 5% CO2. Cells were maintained on culture-ware (including transwells) coated with Matrigel growth factor reduced (MGFR, 50 μg/mL overnight at 4°C and 1 h at 37°C, cat. 354230, Corning) and passaged by 0.25% trypsin digestion (ThermoScientific) before reaching confluency.

extract_protocol:
Genomic DNA was extracted using Quick-gDNA MidiPrep (Zymo Research) following manufacturer's instructions
Genomic DNA amplification for Next Generation Sequencing analysis was performed according to Joung et al. (10.1038/nprot.2017.016)
Library preparation for Next Generation Sequencing analysis was performed according to Joung et al. (10.1038/nprot.2017.016)

treatment_protocol: Cells were transduced with the Human Genome-Scale CRISPR Knock-Out (GeCKO) lentiviral pooled library (GeCKO v2, library A, cat. 1000000048, Addgene), and cultured either in standard flasks or in transwell devices.

tag: cell line

value: fibroblasts

value: Collected from the bottom surface of transwell after the third round of selection


title: DES7S_RiboSeq_rep3

city: Bern

first: Robert

last: Rauscher

state: Bern

address: Freiestrasse 3

institute: University of Bern

data_processing:
Reads were trimmed using the FastX-toolkit. 6 randomized Linkernucleotides at the 3'End and three at the 5'end were trimmed.
Quality of reads was assessed using FastQC (v0.11.7)
Processed reads were mapped against noncoding RNAs and afterward against annotated open reading frames elongated at both ends by 21nt using bowtie (v1.2.3) with settings "-v 1 -m 1 --norc --best --strata
Supplementary files format and content: counts
Library strategy: Ribo-seq

organism: Saccharomyces cerevisiae

source_name: Yeast strain yJD1046

growth_protocol: Yeast cells were grown in YPD media to OD = 0.8. Cells were harvested bySnap freezing, ground in a cryomill and lysates were cleared by centrifugation.

extract_protocol:
Lysates were digested with RNAse1 and 80S ribosomes extracted from a density gradient after Ultracentrifugation. Size excluded RNA fragments were ligated to DeepSeq adapters.
mRNA fragments ranging rom 24-28nt were size excluded and dephosphorylated. Adapters were ligated and the resulting fragments were circularized. cDNA was prepared with circRNA as input and PCR amplicification was performed for 4-8 cycles.

value: plasmid born deltaES7S rRNA sequence

tag: molecule subtype

value: Ribosome protected fragments isolated via densitiy gradients


title: brain, Female, WT, 64


title: Control3

value: Control cultured in standard flask in parallel to the third round of selection


title: control replicate 2


title: DES7S_RiboSeq_rep1

tag: condition


title: Control2

value: Control cultured in standard flask in parallel to the second round of selection


title: Top3

value: Collected from the top surface of transwell after the third round of selection


title: GFKO2.1 colon

description:
Gene expression at day 7 after induction of DSS colitis
GFKO02.1


title: GFKO6 colon

description:
Gene expression at day 7 after induction of DSS colitis
GFKO06


title: Bottom_1

city: Beijing

first: Chao

address: Datun

department: CAS Key Laboratory of Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
1) Merge the double-ended data with FLASH (v1.2.11) to obtain the double-ended reads, and add the unmerged R1 reads to the double-ended reads file to obtain the total clean data;
2)Cut the frame sequence at the left and right ends of the sgRNA using cutadapt (v4.1) to obtain a clean sgRNA fastq sequence with a length of 20 nt and perform quality control using FastQC (v0.11.9);
3) Align the obtained clean sgRNA fastq sequence to the human membrane transporter CRISPRi library sequence with bowtie (v1.3.1), and then convert the sam file into a bam file with samtools to sort and create an index. Bowtie comparison parameters -v 0 -k 1 --best -S;
4) calculate the number of expression counts of sequences in each sgRNA library using the multicov command of bedtools (v2.30.0). Parameters: -f 1.00 -r;
5) Analysis of differentially significant genes between two groups with MAGeCK (v0.5.9.5).
Supplementary files format and content: Excel, top_Bottom_final

growth_protocol: THP-1 cells were obtained from ATCC and cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS, Gibco) and 100 µg ml−1 penicillin-streptomycin.

extract_protocol: Cells were washed in PBS and stored at -80°C for isolation of genomic DNA (gDNA), which was performed with the Blood & Cell Culture DNA Maxi Kit (Qiagen). PCR were performed for identification of sgRNA inserts.

value: Mononuclear cell lines from human peripheral blood

value: the bottom 25% of cBioITA’s intensity


title: brain, Male, Pink1-/-, 25

value: brain

value: Male

value: 8 months


title: Bottom_2


title: brain, Male, WT, 24


title: DES7S_total mRNA_rep3

extract_protocol:
Total RNA extracted by hot acid penol extraction from lysate and mRNA was enriched using OligodT-beads. mRNA was randomly fragmented and ligated to deepSeq adapters.
mRNA fragments ranging rom 24-28nt were size excluded and dephosphorylated. Adapters were ligated and the resulting fragments were circularized. cDNA was prepared with circRNA as input and PCR amplicification was performed for 4-8 cycles.

value: randomly fragment, polyA-enriched mRNA


title: brain, Male, WT, 23


title: Bottom2

value: Collected from the bottom surface of transwell after the second round of selection


title: DES7S_RiboSeq_rep2


title: brain, Male, WT, 22


title: WT_RiboSeq_rep3

value: plasmid born WT rRNA sequence


title: Top_2

value: the top 25% of cBioITA’s intensity


title: brain, Male, WT, 20

value: WT


title: DES7S_total mRNA_rep2

data_processing:
Reads were trimmed using the FastX-toolkit. 6 randomized Linkernucleotides at the 3'End and three at the 5'end were trimmed.
Quality of reads was assessed using FastQC (v0.11.7)
Processed reads were mapped against noncoding RNAs and afterward against annotated open reading frames elongated at both ends by 21nt using bowtie (v1.2.3) with settings "-v 1 -m 1 --norc --best --strata
Supplementary files format and content: counts


title: Top1

value: fibroblasts

value: Collected from the top surface of transwell after the first round of selection


title: GFKO2 colon

description:
Gene expression at day 7 after induction of DSS colitis
GFKO02

value: Colon

value: male

value: Germ-free Card9−/− C57BL/6J

value: DSS


title: Primed MOI75 iPSC_6 (bulkRNA-seq)

first: Akira

last: Kunitomi

state: CA

address: 1650 Owens Street

institute: The J. David Gladstone Institutes

description: Primed induced pluripotent stem cells derived from adult human dermal fibroblasts

data_processing:
FASTQ files were generated from bcl files using bcl2fastq v2.17.1.14 (illumina) and processed using ENCODE long-rna-seq-pipeline v2.3.4.
Sequenced reads were mapped to the human reference genome (GRCh38) using TopHat 2.1.1 or STAR 2.5.1b with GENCODE v24 gene annotations.
Normalized gene expression data was calculated using RSEM 1.2.23.
Gene count data was obtained using featureCounts bundled in Subread 1.5.1.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample.

growth_protocol: Primed PSCs were maintained in StemFit AK02N medium (Ajinomoto) on laminin 511-E8 fragments (iMatrix-511, Nippi)-coated plates. Naive PSCs were cultured on iMEFs and maintained in t2iLGö+Y medium.

extract_protocol:
mRNA or total RNA were extracted from cell lysates using the AllPrep DNA/RNA Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Primed induced pluripotent stem cells

value: Female


title: Control1

value: Control cultured in standard flask in parallel to the first round of selection


title: brain, Male, Pink1-/-, 18

value: brain


title: DES7S_total mRNA_rep1

value: plasmid born deltaES7S rRNA sequence


title: WT_RiboSeq_rep1

value: Ribosome protected fragments isolated via densitiy gradients


title: Primed MOI75 iPSC_5 (bulkRNA-seq)

source_name: Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: Bottom1

value: Collected from the bottom surface of transwell after the first round of selection


title: NCIH929 24 hours AU15330 2

city: Bethesda

first: David

last: Huang

state: Maryland

address: 9000 Rockville Pike

institute: National Cancer Institute

description: TREATMENT

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 human genome using STAR2
Raw read counts per gene were called with Htseq-Count
normalized by DEseq2
Assembly: hg19
Supplementary files format and content: Tab-delimited text files of normalized gene expression

source_name: cell line

growth_protocol: NCIH929 and SKMM1 cells were grown in advanced RPMI supplemented with 4% FBS with pen/strep and glutamine.

extract_protocol:
RNA was extracted using the Qiagen AllPrep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The myeloma cell lines NCIH929 and SKMM1 were grown at 0.5 x 10^6 cells/ml and either treated with DMSO or 1000 nM AU15330 for 6 or 24 hours.  1 x 10^6 cells were collected for each sample.

value: cell line

value: human multiple myeloma

value: 24 hr


title: Primed MOI75 iPSC_7 (bulkRNA-seq)


title: ArR_30min_3, RNA-seq

city: Tianjin

first: Tong

last: Hao

state: China

department: College of Life Sciences

institute: College of Life Sciences, Tianjin Normal University

data_processing:
The original image data were transferred into sequencing data by base calling and generate raw reads.
Clean data including clean reads were obtained by removing the raw reads which contains an adapter, poly-N or with low quality.
Subsequently, Q20, Q30 and GC contents of the clean data were calculated for the quality control.All the downstream analysis was based on the high quality clean data.
Artemia genome from NCBI database was used as the reference genome for genome mapping. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. The FPKM of each gene was calculated based on the length and reads count mapped to the gene. FPKM is the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced.
Assembly: ASM3288406v1
Supplementary files format and content: txt file contains the raw count for genes in each sample
Supplementary files format and content: txt file contains the fpkm values for genes in each sample

organism: Artemia parthenogenetic lineage

source_name: cyst

growth_protocol: Artemia parthenogenetica cysts (provided by Asian Regional Artemia Reference Center, ARARC) were collected in Ebinur Lake and reactivated after dehydration and refrigeration treatment to break diapause.

extract_protocol:
The total RNA from Artemia cysts was isolated using TRIzol reagent and treated with RNase-free DNase I to remove any contaminating genomic DNA. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
Sequencing libraries were generated using a NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using a TruSeq PE Cluster Kit v3-cBot-HS (Illumina). After cluster generation, the library preparations were sequenced on an Illumina novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: At 30min after diapause breaking, the dry cysts were thoroughly rehydrated in ice-cold 30‰ artificial seawater and reactivated in 30‰ artificial seawater at 28 °C under continuous illumination. Each sample was quickly collected and put in liquid nitrogen immediately and then preserved in a −80 °C refrigerator.

value: cyst

value: WT

value: 30min after embryonic diapause termination (EDT)


title: Primed MOI75 iPSC_8 (bulkRNA-seq)

city: San Francisco


title: WT_RiboSeq_rep2

value: plasmid born WT rRNA sequence


title: WT_total mRNA_rep3

value: randomly fragment, polyA-enriched mRNA


title: Top2

value: fibroblasts

value: Collected from the top surface of transwell after the second round of selection


title: brain, Male, Pink1-/-, 17

value: Male

value: 8 months


title: Primed MOI75 iPSC_4 (bulkRNA-seq)

value: Primed induced pluripotent stem cells

value: Female


title: ArR_30min_2, RNA-seq


title: Top_1

value: Mononuclear cell lines from human peripheral blood

value: the top 25% of cBioITA’s intensity


title: wt_2day_CUTTag_rep2

city: hangzhou

first: Zhaoming

last: Ye

address: 88 jiefang road

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
Paired-end 150 bp reads of RNA-seq data were aligned to mm9 genome reference (UCSC) using STAR alignment tool (version 2.7.3a) . Uniquely mapped reads were employed to quantify gene expression using RSEM software (version 1.3.1) . Transcripts per million mapped reads (TPM) were calculated to estimate the gene expression levels, normalized for sequencing depth. Euclidean distance based on TPM values were used to evaluate the similarities across biological replicates. Differential gene expression (DGE) analysis was performed using DESeq2 R package
Raw reads of ATAC-seq data were trimmed  using TrimGalore (version 0.6.1). Trimmed reads were aligned to mm9 genome reference (UCSC) using Bowtie2 aligner.uniquely mapped reads were employed to carry out peak calling using MACS2. Genomic distribution of ATAC peaks was annotated by “ChIPseeker” R package
The CUT&Tag reads were aligned to the mm10 genome by using Bowtie2. Low-mapping-quality reads were filtered by SAMtools (v.1.9), and duplicate reads were removed by Picard tools (v1.90).MACS2 (41) was used to call  peaks with a q-value < 0.01. BigWig files were generated by deeptools (46) by theRPKM normalization method and visualized in igv (v.2.13.1)
Assembly: mm9，mm10

source_name: bone-marrow-derived macrophage

extract_protocol:
Total RNA was extracted using Trizol reagent kit(Invitrogen). Total RNA transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530)
Genomic DNA was extracted after tagementation of Tn5 transposome. Barcoded libraries were then amplified with PCR reactions (TruePrep DNA Library Prep Kit V2 for Illumina, Vazyme)
Genomic DNA was extracted after tagementation of PAG-Tn5 and the libraries were constructed with CUT&Tag Assay Kit (pAG-Tn5) for illumina, (Abclonal)
Total RNA transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530)
ATAC-seq libraries were then amplified with PCR reactions (TruePrep DNA Library Prep Kit V2 for Illumina, Vazyme)
CUT&Tag libraries were constructed with CUT&Tag Assay Kit (pAG-Tn5) for illumina, (Abclonal)
RNA-seq; ATAC-seq; CUT&Tag

value: bone-marrow-derived macrophage

value: Osteoclastic differentiation

value: Day 2

tag: chip antibody


title: NCIH929 24 hours AU15330 1

description: TREATMENT

value: cell line

value: human multiple myeloma

value: 24 hr


title: WT_total mRNA_rep2


title: Primed MOI75 iPSC_3 (bulkRNA-seq)


title: NCIH929 24 hours DMSO 1

description: CTRL

value: DMSO


title: NCIH929 24 hours DMSO 2

description: CTRL


title: Primed MOI75 iPSC_2 (bulkRNA-seq)


title: Primed MOI75 iPSC_1 (bulkRNA-seq)


title: Time 0

value: Collected at the start of the screening


title: ArR_30min_1, RNA-seq

value: cyst

value: WT

value: 30min after embryonic diapause termination (EDT)


title: ArR_30min_3, ATAC-seq

data_processing:
Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2).
These reads were aligned to the Artemia genome using BWA, with standard parameters.
These reads were then filtered for high quality with MAPQ≥13 (i.e. p≤0.05), non-mitochondrial chromosome, and properly paired reads (longer than 18 nt).
FastAC was used to evaluate the quality of the data.
Macs2 software was used for peak calling.
Assembly: ASM3288406v1
Supplementary files format and content: excel file contains the raw count, RPM values, gene ID and transcript ID for each peak
Supplementary files format and content: peak.xlsx

extract_protocol:
nuclei were extracted from each sample, and the nuclei pellet was re-suspended in the Tn5 transposase reaction mix.The transposition reaction was incubated at 37°C for 30 min. Equimolar adapter 1 and adapter 2 were added after transposition.
PCR was then performed to amplify the libraries. After the PCR amplification, libraries were purified with the AMPure beads and the quality of libraries was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 150 bp paired-end reads were generated.


title: SKMM1 24 hours AU15330 2

description: TREATMENT


title: wt_0day_CUTTag_rep2

value: Day 0


title: SKMM1 24 hours AU15330 1

description: TREATMENT


title: Primed MOI15 iPSC_8 (bulkRNA-seq)


title: wt_0day_CUTTag_rep1


title: Primed MOI15 iPSC_7 (bulkRNA-seq)


title: ko_4d_ATACseq_rep2

value: Arid1a Knock out

value: Day 4


title: SKMM1 24 hours DMSO 2

description: CTRL


title: SKMM1 24 hours DMSO 1

description: CTRL


title: RNA ArR_5h_3

data_processing:
The original image data were transferred into sequencing data by base calling and generate raw reads.
Clean data including clean reads were obtained by removing the raw reads which contains an adapter, poly-N or with low quality.
Subsequently, Q20, Q30 and GC contents of the clean data were calculated for the quality control.All the downstream analysis was based on the high quality clean data.
Artemia genome from NCBI database was used as the reference genome for genome mapping. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. The FPKM of each gene was calculated based on the length and reads count mapped to the gene. FPKM is the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced.
Assembly: Artemia genome from NCBI database
Supplementary files format and content: excel file contains the raw count and fpkm values for each sample

treatment_protocol: For diapause stage and 5 h after diapause breaking, the dry cysts were thoroughly rehydrated in ice-cold 30‰ artificial seawater and reactivated in 30‰ artificial seawater at 28 °C under continuous illumination. Each sample was quickly collected and put in liquid nitrogen immediately and then preserved in a −80 °C refrigerator.

value: Artemia parthenogenetica

value: the dry cysts were thoroughly rehydrated in ice-cold 30‰ artificial seawater and reactivated in 30‰ artificial seawater at 28 C under continuous illumination.


title: Primed MOI15 iPSC_6 (bulkRNA-seq)

value: Primed induced pluripotent stem cells

value: Female


title: brain, Male, Pink1-/-, 19

value: brain

value: Male

value: 8 months


title: RNA ArR_5h_2


title: Primed MOI15 iPSC_5 (bulkRNA-seq)


title: ko_4d_ATACseq_rep1

value: bone-marrow-derived macrophage

value: Osteoclastic differentiation


title: ko_2d_ATACseq_rep2

value: Day 2


title: wt_2day_CUTTag_rep1


title: NCIH929 6 hours AU15330 2

description: TREATMENT

value: cell line

value: human multiple myeloma

value: 6 hr


title: NCIH929 6 hours AU15330 1

description: TREATMENT


title: ArR_30min_2, ATAC-seq

value: cyst

value: WT

value: 30min after embryonic diapause termination (EDT)


title: RNA ArR_5h_1


title: Primed MOI15 iPSC_3 (bulkRNA-seq)


title: RNA ArD_0h _3

value: no treatment


title: ko_2d_ATACseq_rep1

value: Arid1a Knock out


title: ArR_30min_1, ATAC-seq


title: ko_0d_ATACseq_rep1

value: Day 0


title: NCIH929 6 hours DMSO 1

description: CTRL

value: DMSO


title: ko_0d_ATACseq_rep2


title: Primed MOI15 iPSC_2 (bulkRNA-seq)

value: Primed induced pluripotent stem cells

value: Female


title: NCIH929 6 hours DMSO 2

description: CTRL


title: RNA ArD_0h _2

value: Artemia parthenogenetica


title: Primed MOI15 iPSC_1 (bulkRNA-seq)


title: Primed MOI15 iPSC_4 (bulkRNA-seq)


title: wt_4d_ATACseq_rep2

value: Day 4


title: SKMM1 6 hours AU15330 2

description: TREATMENT


title: ArR_5h_3

data_processing:
Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2).
These reads were aligned to the Artemia genome using BWA, with standard parameters.
These reads were then filtered for high quality with MAPQ≥13 (i.e. p≤0.05), non-mitochondrial chromosome, and properly paired reads (longer than 18 nt).
FastAC was used to evaluate the quality of the data.
Macs2 software was used for peak calling.
Supplementary files format and content: raw count,RPM values,gene ID and transcript ID for each peak

value: the dry cysts were thoroughly rehydrated in ice-cold 30‰ artificial seawater and reactivated in 30‰ artificial seawater at 30 °C under continuous illumination.


title: wt_4d_ATACseq_rep1

value: bone-marrow-derived macrophage

value: Osteoclastic differentiation


title: CLIP_Input

city: Jinan

first: Xihan

last: Liu

state: Shandong

address: Wenhuaxi Road #44

institute: Shandong University

data_processing:
Trimmomatictools (version 0.36) was utilized to trim adaptor and low-quality bases. RNAcentral (rnacentral.org/) was employed to gain clean reads by deleting rRNA.
Then clean reads were mapped to the hg38 genome with TopHat software (v2.0.13).
IGV was used to visualize mapped reads. Piranha (version 1.2.1) software was employed to perform peak calling.
HOMMER (version 4.11) was used to annotate peaks. STREME (version 5.2.0) and MEME (version 5.3.0) were utilized to detect the consensus motif. Motif central enrichment was performed by CentriMo (version 5.3.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include IP-CLIP annotated peak

source_name: HEY

extract_protocol:
FLAG/Spy-tagged PQBP1 overexpression HEY cells were irradiated at 400 mJ/cm2 using UV Crosslinker (UVP, CL-1000). Nucleoprotein Extraction Kit (Sangon) was employed to extract nuclei before lysis. DNA was removed by Turbo DNase (2 U/µl, Invitrogen, AM2238) and RNA was fragmented with 1:200 diluted RNase I (100 U/µl, Invitrogen, AM2295).
Anti-FLAG magnetic beads (MBL, M185-11) were added to the mixed lysate for 1 h at 25 °C. The beads were washed stringently following the protocols and digested with proteinase K (Roche, 3115828001). RNA was purified using the Spin Column RNA Cleanup & Concentration Kit (Sangon), and the library was constructed and sequenced by the Ribobio Biotechnology Company with the NEBNext Ultra RNA Library Prep Kit for Illumina.
CLIP-Seq

value: HEY

value: Human ovarian cancer cells

tag: rip antibody


title: SKMM1 6 hours AU15330 1

description: TREATMENT

value: cell line

value: human multiple myeloma

value: 6 hr


title: wt_2d_ATACseq_rep2

value: WT

value: Day 2


title: CLIP_IP


title: RIP_IP

data_processing:
Fastp (version 0.19.11) software was used to possess raw data to clean data.
Clean reads were aligned to the hg38 genome by BWA mem (v 0.7.17).
MACS2 (version 2.1.0) peak calling software was then used to identify IP enrichment on genome regions (q-value < 0.05).
Peak related genes were annotated by PeakAnnotator.
Homer was used to detect the denovo motif sequence.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
FLAG/Spy-tagged PQBP1 overexpression HEY cells were adopted for RIP-seq by EZ-Nuclear RIP (Cross-Linked) Kit (Merck Millipore). Briefly, cells were harvested and cross-linked by 0.3% formaldehyde. Nuclei were extracted and lysed by nuclei lysis buffer, and DNA was subjected to sonication to shear to 500-1000 bp fragments.
Magnetic beads with anti-FLAG antibody (Cell Signaling Technology) were used to incubate with nuclei lysates. Then DNaseI was adopted to extract RNA. The library was constructed and pair-end sequenced by Novogene Corporation (Beijing, China) on Illumina NovaSeq 6000 platform (Illumina, CA, USA). Agilent Bioanalyzer 2100 system was employed to assess library quality.


title: ArR_5h_1

value: cyst

value: the dry cysts were thoroughly rehydrated in ice-cold 30‰ artificial seawater and reactivated in 30‰ artificial seawater at 28 °C under continuous illumination.


title: SKMM1 6 hours DMSO 1

description: CTRL

value: DMSO


title: ArD_0h _3

value: no treatment


title: wt_2d_ATACseq_rep1


title: SKMM1 6 hours DMSO 2

description: CTRL


title: RIP_Input


title: wt_0d_ATACseq_rep2

value: Day 0


title: wt_0d_ATACseq_rep1